| As a finger-print spectroscopy to characterize the Vibrational level of molecules, Raman spectroscopy was widely used in Physics, Chemistry, Biology and Material Sciences. Surface Enhanced Raman Spectroscopy, SERS in short, took great advantages in many aspect, for instance, enhancing the energy transfer between the substrate and the molecules, avoiding the fluoresce interferences of the background, enlarging the scattering area of the sample, thus, enhancing the Raman signal of the sample, which produced a leap in Raman scattering in the accuracy of detection. Hence, the application of Raman Scattering was enlarged in the field of Biochemistry, Biophysics and Molecular Biology.In our study, Density Functional Theory, DFT in short, was employed. Simulate the vibrations oftheintramolecularbond of different nucleic acid bases by quantitative calculation, and assign the vibration mode of the solid Raman spectroscopy according to the experiment, which laid the theoretical foundation in the coming study of nuclear acid (enzyme) molecular. Compare the frequency of the theory and experiment, we've found that by employing B3LYP/6-311++G(d,p) as our parameter to calculate was more accuracy than the previous B3LYP/6-311 G(d,p) and B3LYP/6-31++G(d,p), and the theoretical Raman spectroscopy got was better consistent with the experimental one, and the error between Raman peak predicted and the actual was less than 2%.Three methods, in situ photo-reduced silver colloids, Lee-Meise silver colloids and silver film were employed to study the enhancement of different silver substrate to nuclear acid bases by SERS, and the spectra were assigned according to the previous studies. The method in situ photo-reduced silver colloids was employed for the first time. We found that there were great changes in the spectra of Adenine and Guanine by in situ photo-reduced silver colloids, compared to the other two methods, while the other three bases were more or less the same in the three methods. Considering the study by Richard A. J. O'Hairs et al.and. Jitendra Kumar et al. that three models were emphasized, two of which were silver ion-Adenine complex models, and the third one was three silver ions-Adenine complex model, combined by N1, N3, and N7 site. DFT quantitative calculation was employed. Compare the theoretical Raman spectroscopy and the actual one, we found that models two silver ions-two Adenine complex and three silver ions-Adenine complex exhibit great similarities with the experimental spectra. Thus, we inferred the reason why the SERS spectra of Adenine exhibit great changes that the two models exist together in in situ photo-reduced silver colloids. The fact that the SERS spectra of purines varies greatly and the spectra of pyridine resembles greatly also proved that the complex between purine and silver ions was more easily to form. Comparing the three methods, Lee-Meisel method was the best. And this one was choose as our substrate in the study of the SERS spectra of oligonucleotide.Based on the study of the SERS spectroscopy of nuclear acid bases, we carried out the latter experiment on nuclear acid molecules. Firstly, according to the Phan AT et al., we tested four kinds of telometric DNA which were rich in G-quadruplex by means of SERS. In the presences of K+, the telomere sequence was more likely to form the G-quadruplex structure rich in antiparallel loops, which was benefit to the combination of silver ions and Guanine, thus influence the SERS spectra. When compare the Raman spectra of the four telometric DNA in Na+ buffer and K+ buffer, we found that the peak at 1382cm-1 changed greatly, which could be regarded as a key feature whether the G-quadruplex structure was formed. Secondly, together use the means of SERS spectra, RNAfold theoretical prediction, circular dichroism (CD), differential scanning calorimetry (DSC) and autoradiography to study the detail of the stem-loop structure 10-23 deoxyribozyme we designed named SLD deoxyribozyme. The results have proved that the 10-23 SLD could exhibit three different conformations in 10℃,25℃and 40℃, and the Tm of the deoxyribozymes kept at 10℃and 40℃were 45℃and 60℃. the deoxyribozymes kept at 25℃has two Tm, 45℃and 60℃. The deoxyribozyme kept at 10℃and 25℃released more energy when melting. We could concluded that the structure of the deoxyribozyme kept at 10℃and 25℃was more complex. In vitro experiments and autoradiography were carried out under near physiological conditions to compare the catalytic activities of the different deoxyribozymes with different conformations. The results showed that the more complex the structure, the lower activity it exhibits. Finally, we studied the interaction between TMPyP4 porphyrin and 10-23 HQD, by means of UV-Vis spectroscopy, circular dichroism (CD), differential scanning calorimetry (DSC) and Surface Enhanced Raman Spectroscopy (SERS) and analyzed the catalytic activity of 10-23HQD with different ratio of TMPyP4 porphyrin by autoradiography. The UV spectroscopy showed that the porphyrin could intercalate into the G-quadruplex exist in the stem part of the 10-23HQD. The result of Raman spectroscopy showed that the porphyrin molecule could intercalate into the G-quadruplex completely, and the key atom in this process between porphyrin and deoxyribozyme could be the Cm atom of the pyrrole ring of porphyrin. The results of CD and DSC stated that when increase the ratio of pophyrin to deoxyribozyme, the G-quadruplex structure of deoxyribozyme turned from mix structure to antiparallel structure gradually, and the thermal stability enhanced greatly. Finally, the in vitro cleavage experiments proved that during the interaction process of the porphyrin and the deoxyribozyme, the stability of the deoxyribozyme increased slightly, and the activity was decreased even inactive.
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